WordPress core supports auto-embedding videos from Youtube and other video site links. It also understands the messier links that can be copy-pasted from the browser's address bar, such as http://www.youtube.com/watch?NR=1&feature=endscreen&v=[videoid].

I will add support for this soon. Embedding other messy types of links like http://www.youtube.com/user/[user]?feature=watch#p/a/u/0/[videoid] isn't supported by WordPress core. Please let me know if a plugin allows embedding videos with link types that are not yet supported by Video Thumbnails and I'll include support for them in my next patch.

This is also supposed to take care of any videos embedded using plugins with their own shortcode or URL structure, but for some reason this isn't always the case. Maybe try testing out this section to see if it is in fact converting most videos from the core and plugins to their embed code.